PXD024889

PXD024889 is an original dataset announced via ProteomeXchange.

Title	Sulfur-fueled chemolithoautotrophs replenish organic carbon inventory in groundwater
Description	Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity. Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.
HostingRepository	PRIDE
AnnounceDate	2022-05-20
AnnouncementXML	Submission_2022-05-19_22:42:52.483.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-21 23:49:26	ID requested
⏵ 1	2022-05-19 22:42:53	announced

Taubert M, Overholt WA, Heinze BM, Matanfack GA, Houhou R, Jehmlich N, von Bergen M, R, ö, sch P, Popp J, K, ü, sel K, fixation and organic carbon uptake: mixotrophs in modern groundwater. ISME J, 16(4):1153-1162(2022) [pubmed]

submitter keyword: Metaproteomics, Metagenomics, Raman microspectroscopy, Chemolithoautotrophy, Groundwater, Stable isotope probing

Nico Jehmlich
contact affiliation	Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15, 04318 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD024889

PRIDE project URI

• PRIDE
  1. PXD024889
     1. Label: PRIDE project
     2. Name: Sulfur-fueled chemolithoautotrophs replenish organic carbon inventory in groundwater